In my opinion, the design of the site should be as neutral as possible with respect to genre and style. This isn't a suggestion, but rather a sort of meta-criterion that I think should be applied to any design for the site.
The reason for this is that the anime community is very broad in terms of interests. Even looking at the site we've already made, this is apparent. There are a number of users who are primarily interested in action series like naruto and bleach. There are also a lot of users with almost no interest in these shows, who instead watch romance, comedy, drama, etc. (I fall into this category). There are people who only read manga, and people who only watch anime, and everything in between.
I've seen sites before which put a bigger emphasis on one or another style or genre in their site design, and this strongly correlates with what sort of a community they have. The sites where one genre or style are emphasized in the design tend to not seem very inviting to people who are not fans of that. We've talked a lot in chat about what effect the questions which show up to new users have on who we're attracting and whether it creates an environment which doesn't seem inviting to them. Having the site design itself do that would be quite a bit more significant in terms of who we're bringing in. If we want to make a site which is really for the whole anime/manga community, that isn't a good idea.
That doesn't mean that I think we should have a totally bland design, like e.g. MathOverflow, but that the design elements that do get modified are fairly unobtrusive and generic. For an example which I think would be problematic, the banner on RPG is really focused on action, which is fine for an RPG site but would not be for an anime site.
The most successful anime sites online in terms of broad appeal are probably MyAnimeList, Hummingbird, and Anime News Network, which have fairly bland looking designs with some images of particular series. We can't do exactly that, but the design should aim to be similarly reserved to those sites in my opinion.